Undesired different results with bevel modifier and vertex group
I found a reason.
Its because I have another window right next to this. So the vertexes are connected and take the edge in count when beveling so I would have to add another edge between them to separate or the better solution was as @lemon wrote to use edge weight.
Beveled by edge weight

When add a weight between the windows it makes the same artifacts like when I used vertex group that counted in that edges between windows.